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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgataatgacattatagatatatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAG

Basic information

species Glycine max
transcript GLYMA05G34360.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34360.3 (Glycine max), 3'ss of exon 8
lower sequence: AT3G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------gtgagttgataatgacattatagatatatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAG
                   ||| |  ||  | | |   |  | |  |  |   | |   ||   || ||  || | ||  |  ||   |  |   ||||| || || ||  |||| || |||| ||||||||| ||||||||||| ||||||||  | ||||||||||| || |||||||||
gtgatgtaccgttctcatttgattgcatcttaaaaccttgtagagttgagagatatatcatgacacattcaatctttttcatgaatcatgacacacagGTGTCACTTGCCACTGATTTCATGTACAACTACTTTTCAAGAGATGTAACAGCTAGTGTGGGTTATGACTATATGCTTAGACAG

upper sequence: GLYMA05G34360.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------------gtgagttgataatgacatt-------atagatatatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAG
                                                          || |||| |  |||  ||       || |||   ||     |||   ||  |   |||||||| ||    |   | || | |  |||||||| ||||||| || || |||| ||| ||  |||||||||||||||| || || ||||||||||| ||||||||| |||||
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctag--ttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|192329088|gb|FK019731.1|FK019731
EST:     CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
EST: gi|31311896|gb|CD397099.1|CD397099
EST:     CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
EST: gi|193412024|gb|FK379075.1|FK379075
EST:     TAGTCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTAACTTGTCAAGAGATGTCAC
genomic: TAG-CACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACT-ACTTGTCAAGAGATGTCAC
EST: gi|120532642|gb|EH260775.1|EH260775
EST:     CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
EST: gi|120533441|gb|EH261574.1|EH261574
EST:     CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
EST: gi|209707360|gb|BW670910.1|BW670910
EST:     CTAGCACTGGAAT-GTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
EST: gi|207734720|gb|GD710151.1|GD710151
EST:     CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATG
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATG
EST: gi|192322688|gb|FK015025.1|FK015025
EST:     CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAG                         GTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA
genomic: CTAGCACTGGAATGGTTCTTCTAAGCTATGTTCAGAAGGTATCTGAGAAGgtgagttgat ... ttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAG
                                           tgttcctttc  CT-rich tract
          ttttcaattgaacttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgataatgacattatagatatatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG